Histones of Chlamydomonas reinhardtii (Synthesis, Acetylation, and Methylation)

Waterborg, Jakob H.; Robertson, A; Tatar, D L; Borza, Corina M.; Davie, James R.

doi:10.1104/pp.109.2.393

Cited by 49 publications

(67 citation statements)

References 33 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…However, using antibodies specific for H3K9me2 or H4K20me2, we were unable to detect a signal corresponding to histones H3 or H4, respectively (data not shown). This is in agreement with previous data indicating that Chlamydomonas may not contain significant amounts of dimethyl H3K9 (Waterborg et al, 1995). When we examined the global levels of H3K9me1, all strains behaved similarly to the wild type ( Figure 4D).…”

Section: Deletion Of Mut11 Causes Global Changes In H3k4 Methylationsupporting

confidence: 81%

“…Under normal Chlamydomonas growth conditions, 81.2% of histone H3 is monomethylated at K4, and 15.6% shows K9 monomethylation (Waterborg et al, 1995). Consistent with our ChIP results, the extensive amount of H3K4me1 (equivalent to the silenced chromatin fraction) strongly indicates that this modification is associated with repressed chromatin.…”

Section: H3k4 Monomethylation and Euchromatin Silencingsupporting

confidence: 79%

“…These beads were subsequently washed with 25 mL Calmodulin binding buffer (Rigaut et al, 1999) followed by 5 mL of methylase activity buffer (Rea et al, 2000). Proteins retained on the sepharose beads were incubated, in 40 mL of methylase activity buffer, with 250 nCi of the methyl donor 14 C-SAM (Amersham) and 10 mg of Chlamydomonas core histones (Waterborg et al, 1995) or 10 mg of calf thymus histones (Roche) (Rea et al, 2000). After 60 min at 308C, samples were resolved by SDS-PAGE on 15% gels, stained with Coomassie Brilliant Blue, and dried onto filter paper.…”

Section: Hmtase Assaysmentioning

confidence: 99%

See 2 more Smart Citations

Monomethyl Histone H3 Lysine 4 as an Epigenetic Mark for Silenced Euchromatin in Chlamydomonas

et al. 2005

View full text Add to dashboard Cite

Histone Lys methylation plays an important role in determining chromatin states and is mostly catalyzed by SET domaincontaining proteins. The outcome, transcriptional repression or activation, depends on the methylated histone residue, the degree of methylation, and the chromatin context. Dimethylation or trimethylation of histone H3 Lys 4 (H3K4me2 or H3K4me3) has been correlated with transcriptionally competent/active genes. However, H3K4 methylation has also been implicated in gene silencing. This dualistic nature of the H3K4 methyl mark has thus far remained unresolved. In the green alga Chlamydomonas reinhardtii, Mut11p, related to a subunit of trithorax-like methyltransferase complexes, is required for transcriptional silencing. Here, we show that Mut11p interacts with conserved components of H3K4 methyltransferase machineries, and an affinity-purified Mut11p complex(es) methylates histones H3, H2A, and H4. Moreover, a Mut11 mutant showed global loss of monomethylated H3K4 (H3K4me1) and an increase in dimethylated H3K4. By chromatin immunoprecipitation analysis, this strain also displayed substantial reduction in H3K4me1 and enrichment in H3K4me2 associated with transcriptionally derepressed genes, transgenes, and retrotransposons. RNA interference-mediated suppression of Set1, encoding an H3K4 methyltransferase, induced similar phenotypes, but of lower magnitude, and no detectable increase in H3K4me2. Together, our results suggest functional differentiation between dimethyl H3K4 and monomethyl H3K4, with the latter operating as an epigenetic mark for repressed euchromatin.

show abstract

Section: Deletion Of Mut11 Causes Global Changes In H3k4 Methylationsupporting

confidence: 81%

Section: H3k4 Monomethylation and Euchromatin Silencingsupporting

confidence: 79%

Section: Hmtase Assaysmentioning

confidence: 99%

See 1 more Smart Citation

Monomethyl Histone H3 Lysine 4 as an Epigenetic Mark for Silenced Euchromatin in Chlamydomonas

et al. 2005

View full text Add to dashboard Cite

show abstract

“…In some eukaryotes including C. reinhardtii, monomethylation of lysine 4 in histone H3 (H3K4) and monomethylation of H3K9 are putative epigenetic markers for a transcriptionally silent/inactive chromatin state (Cheung and Lau 2005;Van Dijk et al 2005;Waterborg et al 1995;Casas-Mollano et al 2007;Pfluger and Wagner 2007), and the underlying DNA in heterochromatin is often accompanied by methylation. In contrast, histones located in euchromatic regions usually have different types of modifications, such as acetylation, and the DNA in these regions is usually not highly methylated.…”

mentioning

confidence: 99%

Unstable RNAi Effects Through Epigenetic Silencing of an Inverted Repeat Transgene in Chlamydomonas reinhardtii

2008

View full text Add to dashboard Cite

RNA interferences in the unicellular green alga, Chlamydomonas reinhardtii, can be silenced. We have used the silencing of a transgene (aadA) that confers resistance to spectinomycin to investigate the mechanisms responsible for silencing by an artificial inverted repeat (IR) of the aadA gene. The IR construct provided strong silencing, but the RNAi efficiency varied among subclones of a single RNAitransformed strain with successive cell divisions. Northern blot analyses revealed an inverse correlation between the copy number of the hairpin RNA and the spectinomycin resistance of the subclones. There is an inverse correlation between the efficiency of RNAi and the frequency of methylated CpG (*CpG) in the silenced region. No significant methylated cytosine was observed in the target aadA gene, which suggests the absence of RNA-directed DNA methylation in trans. Several experiments suggest the existence of an intrinsic IR sequence-dependent but a transcription-independent DNA methylation system in C. reinhardtii. The correlation between the *CpG levels and the IR transcript implies the existence of IR DNA-dependent DNA methylation. Treatment of RNAi-induced cells with a histone deacetylase inhibitor, Trichostatin A, rapidly increased the amount of the hairpin RNA and suggests that transcription of the silencer construct was repressed by *CpG-related silencing mechanisms.

show abstract

“…Proteins were quantitated by densitometry of gels, stained with Coomassie Brilliant Blue R-250, and destained in 7% acetic acid, 20% methanol. Specific radioactivity was determined by densitometry of fluorographic exposures exactly as described (17,18).…”

Section: Methodsmentioning

confidence: 99%

Identification of a Replication-independent Replacement Histone H3 in the Basidiomycete Ustilago maydis

Verma

Kapros

Waterborg

2011

Journal of Biological Chemistry

View full text Add to dashboard Cite

Ustilago maydis is a haploid basidiomycete with single genes for two distinct histone H3 variants. The solitary U1 gene codes for H3.1, predicted to be a replication-independent replacement histone. The U2 gene is paired with histone H4 and produces a putative replication-coupled H3.2 variant. These predictions were evaluated experimentally. U2 was confirmed to be highly expressed in the S phase and had reduced expression in hydroxyurea, and H3.2 protein was not incorporated into transcribed chromatin of stationary phase cells. Constitutive expression of U1 during growth produced ϳ25% of H3 as H3.1 protein, more highly acetylated than H3.2. The level of H3.1 increased when cell proliferation slowed, a hallmark of replacement histones. Half of new H3.1 incorporated into highly acetylated chromatin was lost with a half-life of 2.5 h, the fastest rate of replacement H3 turnover reported to date. This response reflects the characteristic incorporation of replacement H3 into transcribed chromatin, subject to continued nucleosome displacement and a loss of H3 as in animals and plants. Although the two H3 variants are functionally distinct, neither appears to be essential for vegetative growth. KO gene disruption transformants of the U1 and U2 loci produced viable cell lines. The structural and functional similarities of the Ustilago replication-coupled and replication-independent H3 variants with those in animals, in plants, and in ciliates are remarkable because these distinct histone H3 pairs of variants arose independently in each of these clades and in basidiomycetes.Core histones provide the packaging proteins for DNA in eukaryotic cells. During the S phase when genomic DNA is duplicated, replication-coupled expression of histone genes provides new protein to assemble newly replicated DNA. Histone chaperones assist in the creation of new nucleosomes to maintain a stable, compacted, repressed state of chromatin. Within this context, regulatory proteins modulate chromatin environments to facilitate access to the DNA for gene transcription. The components and processes that allow RNA polymerases to transcribe a chromatin template, such as epigenetic modifications of DNA and histones, are being identified and intensely studied. The processes of nucleosome displacement from DNA by transcribing RNA polymerases and of nucleosome reassembly from available histones remain poorly understood.In research going back decades, it was observed that the composition of nucleosomes across transcribed gene regions, identified in part by high levels of histone acetylation, changed over time. Replication-coupled (RC) 2 histone H3 variants like H3.2 in birds were replaced by histone H3.3, a constitutively expressed form of animal histone H3. This histone is now known as a replacement histone or as a replication-independent (RI) H3 variant (1, 2). Specialized chaperones such as HIRA and Daxx selectively bind these RI H3 proteins at a small region, residues 87-90, which is uniquely different between RI and RC forms (3, 4). In the S phase...

show abstract

Histones of Chlamydomonas reinhardtii (Synthesis, Acetylation, and Methylation)

Cited by 49 publications

References 33 publications

Monomethyl Histone H3 Lysine 4 as an Epigenetic Mark for Silenced Euchromatin in Chlamydomonas

Monomethyl Histone H3 Lysine 4 as an Epigenetic Mark for Silenced Euchromatin in Chlamydomonas

Unstable RNAi Effects Through Epigenetic Silencing of an Inverted Repeat Transgene in Chlamydomonas reinhardtii

Identification of a Replication-independent Replacement Histone H3 in the Basidiomycete Ustilago maydis

Contact Info

Product

Resources

About